Ratio of bases with quality value exceeded 30 in the sequenced reads
CID Q30
Ratio of CID (Coordinate ID) bases with quality value exceeded 30
MID Q30
Ratio of MID (Molecule ID) bases with quality value exceeded 30
Total Reads
2,050,261,820
Total Q30
84.13%
CID Q30
86.65%
MID Q30
80.82%
Annotation
Exonic
Number of reads that mapped uniquely to an exonic region and on the same strand of the genome
Intronic
Number of reads that mapped uniquely to an intronic region and on the same strand of the genome
Intergenic
Number of reads that mapped uniquely to an intergenic region and on the same strand of the genome
Transcriptome
Number of reads that mapped to a unique gene in the transcriptome. These reads are considered for MID counting. (Transcriptome = Exonic + Intronic)
Antisense
Number of reads mapped to the transcriptome but on the opposite strand of their annotated gene
Exonic
739,656,914
Intronic
43,255,908
Intergenic
165,725,909
Transcriptome
782,912,822
Antisense
187,759,357
RNA Mapping
Clean Reads
Number of Valid CID Reads that have passed QC
Uniquely Mapped Reads
Number of reads that mapped uniquely to the reference genome
Multi-Mapped Reads
Number of reads that mapped more than one time on the genome
Unmapped Reads
Number of reads that cannot be mapped to the reference genome
Clean Reads
1,198,716,897
Uniquely Mapped Reads
948,638,731
Multi-Mapped Reads
172,206,031
Unmapped Reads
77,872,135
Tissue
DNB Under Tissue
Number of DNBs under tissue coverage region
mRNA-Captured DNBs Under Tissue
Number of DNBs under tissue that have captured mRNA
Genes Under Tissue
Number of detected gene under tissue coverage
Number of MID Under Tissue Coverage
Number of MID under tissue coverage
Fraction MID in Spots Under Tissue
Fraction of MID under tissue over total unique reads (MID Under Tissue / Unique Reads)
Reads Under Tissue
Number of reads with position prior to filtration under tissue coverage
Fraction Reads in Spots Under Tissue
Fraction of mapped reads under tissue over total mapped reads (Mapped Reads in Spots Under Tissue / (Valid CID Reads + Discarded MID Reads))
DNB Under Tissue
65,053,625
mRNA-Captured DNBs Under Tissue
30,070,646
Genes Under Tissue
27,092
Number of MID Under Tissue Coverage
95,868,327
Fraction MID in Spots Under Tissue
56.53%
Reads Under Tissue
794,286,182
Fraction Reads in Spots Under Tissue
49.69%
Sequencing Saturation
(left) Plot of the sequencing saturation as a function of sequencing depth(bin200)
(middle) Plot of the median number of genes detected per bin as a function of sequencing depth(bin200)
(right) Plot of the unique reads detected per bin as a function of sequencing depth(bin200)
Tissue Square Bin Statistics
Bin Size
The size of Bin which is the unit of aggregated DNBs in a squared region (i.e. Bin 50 = 50 * 50 DNBs)
Mean Reads (per bin)
Mean number of sequenced reads divided by the number of bins under tissue coverage
Median Reads (per bin)
Median number of sequenced reads divided by the number of bins under tissue coverage (pick the middle value after sorting)
Mean Gene Type (per bin)
Mean number of unique gene types divided by the number of bins under tissue coverage
Median Gene Type (per bin)
Median number of unique gene types divided by the number of bins under tissue coverage
Mean MID (per bin)
Mean number of MIDs divided by the number of bins under tissue coverage
Median MID (per bin)
Median number of MIDs divided by the number of bins under tissue coverage
Bin Size
Mean Reads (per bin)
Median Reads (per bin)
Mean Gene Type (per bin)
Median Gene Type (per bin)
Mean MID (per bin)
Median MID (per bin)
20
4,855
4,899
351
363
586
585
50
30,079
30,297
1,617
1,690
3,630
3,624
100
118,514
119,911
4,120
4,329
14,304
14,315
150
262,660
269,607
6,325
6,694
31,702
32,137
200
460,990
481,129
8,117
8,649
55,640
57,489
Bin 20
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Bin 50
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Bin 100
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Bin 150
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Bin 200
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Clustering
(left) Clustering spots (bin200) under tissue covered with the Leiden algorithm
(right) UMAP projections of spots (bin200) colored by automated clustering. Same color is assigned to spots that are within shorter distance and with similar gene expression profile
Tissue Plot with Spots (bin200)
UMAP Projection of Spots (bin200)
Cell Bin Statistics
Cell Count
Number of cells
Mean/Median Cell Area
Mean/Median cell area (pixel)
Mean/Median DNB Count
Mean/Median number of DNBs that have captured-mRNAs per cell
Mean/Median Gene Type
Mean/Median genes per cell
Mean/Median MID
Mean/Median MID count per cell
Cell Count
73,923
Mean Cell Area
220
Median Cell Area
195
Mean DNB Count
202
Median DNB Count
168
Mean Gene Type
179
Median Gene Type
154
Mean MID
283
Median MID
233
Cell Bin
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, DNB numbers, and cell area (pixel) with rug along the x axis
Clustering
(left) Clustering spots (cell bin) under tissue covered region with the Leiden algorithm
(right) UMAP projections of spots (cell bin) colored by automated clustering. Spots in the short distance are assigned with the same color have similar gene expression profile.
Tissue Plot with Spots (cell bin)
UMAP Projection of Spots (cellbin)
Image Information
Manufacture
motic
Model
MoticamProS5 Lite M
Scan Time
2022-11-2 14:27:40
Overlap
0.1
Exposure Time (ms)
120.262
Scan Rows
7
Scan Columns
7
FOV Height
2,031
FOV Width
2,424
Stain Type
DAPI
Stitched Image
No
Image Name
SS200000059_NC_SC_20230315_170415_2.0.0
Stitching
Template Source Row No.
The row number of the template FOV used for predicting the entire template
Template Source Column No.
The column number of the template FOV used for predicting the entire template
Global Height
Height of the stitched image
Global Width
Width of the stitched image
Template Source Row No.
6
Template Source Column No.
0
Global Height
12,999
Global Width
15,516
QC
ImageQC version
ImageQC version
QC Pass
Whether the image(s) passed imageQC quality check
Track Line Score
Reference score for track line detection
Clarity Score
Reference score for image clarity
Good FOV Count
Number of FOVs that have at least one track dot detected
Total FOV Count
Total number of FOVs
Stitching Score
Reference score for stitching
Tissue Segmentation Score
Reference score for tissue segmentation
Registration Score
Reference score for aligning image with gene expression matrix
ImageQC Version
2.0.0
QC Pass
Pass
Track Line Score
77
Clarity Score
2
Good FOV Count
38
Total FOV Count
49
Stitching Score
100
Tissue Segmentation Score
100
Registration Score
79
Registration
ScaleX
The lateral scaling between image and template
ScaleY
The longitudinal scaling between image and template
Rotation
The rotation angle of the image relative to the template
Flip
Whether the image is flipped horizontally
Image X Offset
Offset between image and matrix in x direction
Image Y Offset
Offset between image and matrix in y direction
Counter Clockwise Rotation
Counter clockwise rotation angle
Manual ScaleX
The lateral scaling based on image center (manual-registration)
Manual ScaleY
The longitudinal scaling based on image center (manual-registration)
Manual Rotation
The rotation angle based on image center (manual-registration)
Matrix X Start
Gene expression matrix offset in x direction by DNB numbers
Matrix Y Start
Gene expression matrix offset in y direction by DNB numbers
Matrix Height
Gene expression matrix height
Matrix Width
Gene expression matrix width
ScaleX
1.005
ScaleY
1.005
Rotation
-4.085
Flip
True
Image X Offset
4,723
Image Y Offset
1,707
Manual ScaleX
-
Manual ScaleY
-
Manual Rotation
-
Counter Clockwise Rotation
0
Matrix X Offset
0.00
Matrix Y Offset
0.00
Matrix Height
23,520
Matrix Width
23,520
Horizontal Image Stitching Deviation Heatmap
Image stitching deviation in the horizontal axis, a lighter color indicates better stitching (the heatmap and frame of axes have been adjusted with the registration parameters)
Vertical Image Stitching Deviation Heatmap
Image stitching deviation in the vertical axis, a lighter color indicates better stitching (the heatmap and frame of axes have been adjusted with the registration parameters)
Analytical Report
